To begin with, Nick Fury does actually appear in the flesh in the MC2, but isn't mentioned by name for several years. Fury is first alluded to in A-Next #5 when, following the unconfirmed appearance of Doctor Doom in Latveria by S.H.I.E.L.D. Agents, the Fantastic Five are tasked with investigating. When Cassie Lang aka Stinger requests the Avengers conduct the investigation instead, Johnny Storm aka the Human Torch is initially reluctant, saying 'The Big Guy himself' had asked them.
A few issues later, while helping the hero Argo to find his father Hercules, the Avengers find themselves in the secret S.H.I.E.L.D. facility within Mount Athena. There they learn 'The Merchandise' (actually Hercules himself) is buried several miles within the mountain in a special Adamantium cell. Hercules identity as 'The Merchandise' is kept strictly need-to-know and none of the S.H.I.E.L.D. Agents at Mount Athena are privy to this information. However, Agent 33 receives orders from 'The Top Man himself' to allow the Avengers to take custody of 'The Merchandise.'
Unless I'm mistaken, we don't get any more mentions of Fury until Amazing Spider-Girl #9 when Maria Hill mentions her 'Superiors' tasking Special Agent Arthur Weadon with securely transporting 'Specimen 297' (actually a piece of the Carnage symbiote) through New York City. When the transport convoy is attacked by a faction of S.H.I.E.L.D. Agents led by Contessa Valentina Allegra de Fontaine and the Specimen accidentally let loose in the city by Spider-Girl, Carnage is reborn.
Nick Fury makes his first on-panel appearance - albeit shrouded in shadow-when he assures President G.W. Bridge the situation would be resolved despite the complications (Amazing Spider-Girl #10).
It's in Amazing Spider-Girl #12 that we finally see Nick Fury in full and learn the entire plot. As the United States was unwilling to destroy the Carnage symbiote despite the United Nations stance on the use of bio-weapons, G.W. Bridge and Nick Fury organised for the team of disguised S.H.I.E.L.D. Agents to 'steal' the Specimen, setting up Weadon's team to fail.
This was all to demonstrate the dangers to the congressional committee wishing to keep the symbiote for bio-weapon research under the guise of finding a cure for cancer. Despite the operation not going as planned, the situation was salvaged thanks to Spider-Girl's intervention, providing the President with a sound rationale to convince the congressional committee to destroy the remaining Specimen.
As you can see, Fury is still up to his classic spymaster shenanigans, though he appears to prefer to remain in the shadows (both literal and figurative) more than before.
Until I find a nice fitting eyepatch and retire to the darker corners of the MC2, I remain
frogoat